Algorithms and analyses for the evolution of plant chromosomes and gene orders

植物染色体和基因顺序进化的算法和分析

• 批准号: RGPIN-2022-05212
• 负责人: Sankoff, David
• 金额: $ 3.5万
• 依托单位: University of Ottawa
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=759215
• 关键词: Algorithms; analyses; evolution; plant; chromosomes

We study structural genome evolution in terms of gene order, concentrating on the flowering plants. One focus ison branching process models for the expansion and contraction of single gene families through recurrent whole genome doubling and loss of duplicate genes, as well as the nature of this loss in syntenic context via pseudogenization or DNA excision. The other focus is on phylogeny-based ancestral genome reconstruction at the level of gene order within whole chromosomes. Whole-genome doubling, tripling or replicating to a greater degree is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times. When this event occurs in plant genome evolution, it sets in operation a more gradual compensatory process called fractionation, the loss of duplicate genes. We make use of branching process models of recurrent whole genome duplication and fractionation, where the parameters to be estimated are fractionation rates. In the initial development, we tested the analyses on the Malvaceae and the Solanaceae. We plan to implement a full-fledged pipeline with continued developments of our method, and survey a large number of plant families for a comparative study. Adding a syntenic dimension to the study of fractionation, we explore the mechanism of fractionation. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost-there are few if any relics of the missing sequence -"pseudogenes". These must be rare or extremely transient in this context. We have already verified this in ten genomes, but plan to look at  a much wider sample of genome replication events, including very recent ones in the agricultural context.  We will also look to see how frequently apparent deletion is an artifact of gene movement out of, or into, syntenic contexts. A key part of our program is to construct a pipeline 'RACCROCHE" for the phylogeny-based inference of ancestral genomes.   The strategy of this method is to accumulate a large number of generalized gene adjacencies, not just immediate neighbours, from all the extant chromosomes, subject to a phylogenetic filter at each ancestral node of the phylogeny, as input to a maximum weight matching algorithm. The latter outputs "contigs" containing up to several hundred genes each. All pairs of these contigs are then matched against each of the chromosomes in each of the extant genomes to compile a co-occurrence score and a pairwise order. The matrix of scores is then clustered to partition the set of contigs into disjoint, ordered sets,which are naturally interpretable as the chromosomes of the ancestral genome associated with the particular node of the phylogeny. We have done tests on data from the entire monocot clade and from several rosid orders.

我们从基因序列的角度研究结构基因组的进化，主要集中在开花植物上。One Focus ISON分枝过程模型通过循环的全基因组加倍和重复基因的丢失来描述单基因家族的扩展和收缩，以及在共线背景下通过假基因化或DNA切除来解释这种丢失的性质。另一个焦点是在整个染色体内的基因序列水平上基于系统发育的祖先基因组重建。全基因组加倍、三倍或更大程度的复制在开花植物的几乎所有谱系中都得到证明，在一些植物的祖先中重复出现两次、三次或更多次。当这一事件在植物基因组进化中发生时，它启动了一个更渐进的补偿过程，称为分裂，即重复基因的丢失。我们利用循环全基因组复制和分裂的分枝过程模型，其中被估计的参数是分馏率。在最初的开发中，我们对锦葵科和茄科进行了分析。随着我们方法的不断发展，我们计划实施一条成熟的管道，并对大量的植物科进行调查以进行比较研究。在分馏研究中加入共线维度，探讨了分馏的机理。通过检查连续的一系列基因被删除后剩余的序列有多少，我们发现这种残基保持在一个恒定的低水平，与有多少基因丢失无关--丢失的序列的残留物很少--假基因。在这种情况下，这些肯定是罕见的或极其短暂的。我们已经在10个基因组中验证了这一点，但计划查看更广泛的基因组复制事件样本，包括最近在农业背景下的样本。我们还将研究表面缺失是基因移出或移入共时上下文的人工产物的频率。我们计划的一个关键部分是构建一个管道‘Raccroche’，用于基于系统发育的祖先基因组推断。这种方法的策略是从所有现存的染色体中积累大量的广义基因邻接，而不仅仅是直接邻接，并在系统发育的每个祖先节点进行系统发育过滤器，作为最大权重匹配算法的输入。后者输出“重叠群”，每个重叠群包含多达数百个基因。然后，将所有这些重叠群对与每个现存基因组中的每条染色体进行匹配，以编制共生得分和成对排序。然后对分数矩阵进行聚类，以将重叠群集合划分为不相交的有序集合，这些集合自然可以解释为与系统发育的特定节点相关联的祖先基因组的染色体。我们已经对整个单子叶支系和几个玫瑰花目的数据进行了测试。